3D Electron Microscopy (3D-EM) Data Navigator [English / 日本語]
Top Gallery List Diagram Statistics Viewer Documents
Movie pageYodrodumi (structure viewer)
PDBj>EM Navigator>Detail page - EMDB-1122

Visualizing tmRNA entry into a stalled ribosome.

by single particle reconstruction, at 13 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 42, Image by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 42, Image by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-1zc8, Surface level: 42, Image by UCSF CHIMERA

#4: Simplified surface model with fitted atomic model: PDB-1zc8, Image by Jmol

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1122
TitleVisualizing tmRNA entry into a stalled ribosome.
Mapthis is a ribosome consisting 70S + Psite tRNA + mRNA + EF-Tu.GDP + alanylated tmRNA + SmpB + Kirromycin + S1
Sample70S-Psite tRNA - mRNA - EF-Tu.GDP - alanylated tmRNA - SmpB - Kirromycin - S1
AuthorsValle M, Gillet R, Kaur S, Henne A, Ramakrishnan V, Frank J
DateDeposition: 2005-03-24, Header release: 2005-04-11, Map release: 2005-04-11, Last update: 2012-10-24
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 42, Image by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 42, Image by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-1zc8, Surface level: 42, Image by UCSF CHIMERA

#4: Simplified surface model with fitted atomic model: PDB-1zc8, Image by Jmol

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

PDB-1zc8

CiteFit

Cite: data citing same article

Fit: output model of fitting

Similar strucutres
List of similar structure data Omokage searchabout Omokage system
Article
Citation - Primary
ArticleScience, Vol. 300, Issue 5616, Page 127-30, Year 2003
TitleVisualizing tmRNA entry into a stalled ribosome.
AuthorsMikel Valle, Reynald Gillet, Sukhjit Kaur, Anke Henne, V Ramakrishnan, Joachim Frank
Howard Hughes Medical Institute, Wadsworth Center, Health Research, Inc., Empire State Plaza, Albany, NY 12201-0509, USA.
KeywordsAlanine, Anticodon, Bacterial Proteins (metabolism), Codon, Codon, Terminator, Cryoelectron Microscopy, Guanosine Triphosphate (metabolism, 86-01-1), Image Processing, Computer-Assisted, Models, Molecular, Nucleic Acid Conformation, Open Reading Frames, Peptide Elongation Factor Tu (metabolism, 3.6.1.-), Protein Biosynthesis, Pyridones (pharmacology), RNA, Bacterial (chemistry), RNA, Messenger (chemistry), RNA, Transfer (chemistry, 9014-25-9), RNA-Binding Proteins (chemistry), Ribosomal Proteins (chemistry), Ribosomes (metabolism), Thermus thermophilus (chemistry), mocimycin, ribosomal protein S1, small protein B, tmRNA
LinksPubMed: 12677067, DOI: 10.1126/science.1081798
Map
Fileemd_1122.map.gz ( map file in CCP4 format, 10720 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
140 pix
2.82 A/pix
= 394.8 A
140 pix
2.82 A/pix
= 394.8 A
140 pix
2.82 A/pix
= 394.8 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:54.9, 42 (movie #1):
Minimum - Maximum: -147.485 - 313.886
Average (Standard dev.): 2.87458 (28.7702)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions140140140
Origin-70-70-70
Limit696969
Spacing140140140
Unit CellA= B= C: 394.8 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 2.82 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z2.822.822.82
M x/y/z140140140
origin x/y/z0.0000.0000.000
length x/y/z394.800394.800394.800
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-220-220-220
NX/NY/NZ441441441
MAP C/R/S123
start NC/NR/NS-70-70-70
NC/NR/NS140140140
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-147.485313.8862.875
Annotation Detailsthis is a ribosome consisting 70S + Psite tRNA + mRNA + EF-Tu.GDP + alanylated tmRNA + SmpB + Kirromycin + S1
Supplement
Images
Images
Sample
Name70S-Psite tRNA - mRNA - EF-Tu.GDP - alanylated tmRNA - SmpB - Kirromycin - S1
Number of Components5
Component #1: ribosome-prokaryote - 70S Ribosome
Scientific name70S Ribosome
DetailsThermus thermophilus
Scientific Name of SpeciesThermus thermophilus HB8
NCBI taxonomy300852
ProkaryoteALL
Recombinant expressionNo
Component #2: nucleic-acid - tRNA
Scientific nametRNA
DetailsP site
Scientific Name of SpeciesThermus thermophilus HB8
NCBI taxonomy300852
SyntheticNo
StructureSINGLE STRANDED
ClassT-RNA
Component #3: protein - EF-Tu
Scientific nameEF-Tu
Scientific Name of SpeciesThermus thermophilus HB8
NCBI taxonomy300852
Recombinant expressionNo
Component #4: ligand - tmRNA
Scientific nametmRNA
Scientific Name of SpeciesThermus thermophilus HB8
NCBI taxonomy300852
Recombinant expressionNo
Component #5: protein - SmpB
Scientific nameSmpB
Scientific Name of SpeciesThermus thermophilus HB8
NCBI taxonomy300852
Recombinant expressionNo
Experiment
Sample Preparation
Specimen Stateparticle
BufferDetails: 25 mM Hepes-KOH pH 7.5, 30 mM NH4Cl, 7mM MgCl2, 2 mM ATP, 6 mM PEP, 10g/ml PK
pH: 7.5
Vitrification
Cryogen NameETHANE
Humidity90
Temperature93 Kelvin
InstrumentHOMEMADE PLUNGER
MethodBlot for 2 seconds before plunging
DetailsVitrification instrument: two side blotting plunger
Imaging
MicroscopeFEI TECNAI F20
Date2002-8-1
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose15 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 49000, Calibrated: 52000
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus1450 nm - 3700 nm
Specimen Holder
HolderCryo transfer
ModelGATAN LIQUID NITROGEN
Temperature93 K
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
Number of Digital Images44
Sampling Size14
Od Range1.2
Quant Bit Number12
ScannerZEISS SCAI
Processing
Methodsingle particle reconstruction
3D reconstruction
Algorithmreference projection
SoftwareSPIDER
CTF Correctiondefocus groups
Resolution By Author13 A
Resolution MethodFSC at 0.15 cut-off
Euler Angles DetailsSPIDER definition
Single Particle
Number of Projections27644
Applied SymmetryC1 (asymmetric)
Atomic Model Fitting
Model #0
Refinement Protocolrigid body
Target Criteriacross correlation coefficient
Softwaremanual
DetailsProtocol: Rigid Body. The domains were separately fitted by manual docking using program O
Fitted Coordinate
PDB entry ID
Download
Data from EMDB
Header (meta data in XML format)emd-1122.xml (9.2 KB)
Map dataemd_1122.map.gz (9.9 MB)
Images1122.gif (15.1 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1122
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 5.5 MB
Session file for UCSF-Chimera, 26.4 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.9 MB
Session file for UCSF-Chimera, 26.5 KB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 5 MB
Session file for UCSF-Chimera, 207.6 KB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 4.5 MB